Multiple sequence alignment layer for ggplot2. It creats background tiles with/without sequence characters.

geom_msa(
data,
font = "helvetical",
mapping = NULL,
color = "Chemistry_AA",
custom_color = NULL,
char_width = 0.9,
none_bg = FALSE,
by_conservation = FALSE,
posHighligthed = NULL,
seq_name = NULL,
border = NULL,
consensus_views = FALSE,
use_dot = FALSE,
disagreement = TRUE,
ignore_gaps = FALSE,
ref = NULL,
position = "identity",
show.legend = FALSE,
...
)

## Arguments

data sequence alignment with data frame, generated by tidy_msa(). font families, possible values are 'helvetical', 'mono', and 'DroidSansMono', 'TimesNewRoman'. Defaults is 'helvetical'. aes mapping If font = NULL, only plot the background tile. A Color scheme. One of 'Clustal', 'Chemistry_AA', 'Shapely_AA', 'Zappo_AA', 'Taylor_AA', 'LETTER','CN6',, 'Chemistry_NT', 'Shapely_NT', 'Zappo_NT', 'Taylor_NT'. Defaults is 'Chemistry_AA'. A data frame with two cloumn called "names" and "color".Customize the color scheme. a numeric vector. Specifying the character width in the range of 0 to 1. Defaults is 0.9. a logical value indicating whether background should be disaplayed. Defaults is FALSE. a logical value. The most conserved regions have the brightest colors. A numeric vector of the position that need to be highlighted. a logical value indicating whether seqence names should be displayed. Defaults is 'NULL' which indicates that the sequence name is displayed when 'font = null', but 'font = char' will not be displayed. If 'seq_name = TRUE' the sequence name will be displayed in any case. If 'seq_name = FALSE' the sequence name will not be displayed under any circumstances. a character string. The border color. a logical value that opeaning consensus views. a logical value. Displays characters as dots instead of fading their color in the consensus view. a logical value. Displays characters that disagreememt to consensus(excludes ambiguous disagreements). a logical value. When selected TRUE, gaps in column are treated as if that row didn't exist. a character string. Specifying the reference sequence which should be one of input sequences when 'consensus_views' is TRUE. Position adjustment, either as a string, or the result of a call to a position adjustment function, default is 'identity' meaning 'position_identity()'. logical. Should this layer be included in the legends? additional parameter

A list

## Author

Guangchuang Yu, Lang Zhou seq_name' work posHighligthed' work border' work none_bg' work

## Examples

library(ggplot2)
aln <- system.file("extdata", "sample.fasta", package = "ggmsa")
tidy_aln <- tidy_msa(aln, start = 150, end = 170)
ggplot() + geom_msa(data = tidy_aln, font = NULL) + coord_fixed()